[Gate-users] Re: error on installation of lmf_v3.0
Joon Young Suk
joonyoung.suk at gmail.com
Sat Dec 8 12:01:10 CET 2007
Never mind. I figured out.
It was just because my "root" wasn't active properly.
Thanks
Joon Young
On 8-Dec-07, at 2:59 AM, gate-users-request at lists.healthgrid.org wrote:
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> Today's Topics:
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> 1. Re: source angle type (Simon Stute)
> 2. Re: source angle type (Joon Young Suk)
> 3. error on installation of lmf_v3.0 (Joon Young Suk)
>
> From: "Simon Stute" <gate.stute at gmail.com>
> Date: December 7, 2007 5:20:11 PM PST (CA)
> To: "Joon Young Suk" <joonyoung.suk at gmail.com>
> Cc: gate-users at lists.healthgrid.org
> Subject: Re: [Gate-users] source angle type
>
>
> Hi Joon,
>
> Display is just display, not very faithful ... Have you got the
> same results in your root results (or other kind of output results) ??
> I don't see any attenuation volume in your display, did you build
> some ?? Because the 'confine' macro command is usually used to fix
> an 'activity volume' to a geometrical volume (assigned with a
> material) that is moving during the simulation. You have defined
> some cylindrical shape activity volume but in your display, its
> look like that it is a point source 'volume'. What is your complete
> macro file ?
>
> Cheers,
> Simon
>
> 2007/12/7, Joon Young Suk <joonyoung.suk at gmail.com>:
>>
>>>
>>> Hi all,
>>> I am trying to simulate the scan with a cylindrical phantom which
>>> as two rod source inside.
>>> I built two rod sources with cylindrical geometry and set the
>>> angle type as "iso".
>>> I think the LORs should be randomly distributed through all 4pi
>>> angle, but the simulation doesn't look like that.
>>>
>>> From the display during the simulation, I can see most LORs are
>>> lying horizontally on the centre plane.
>>>
>>> Please check the image from the followed link :
>>>
>>> http://www.joonyoung.net/iso.jpg
>>>
>>> Also, here is my code for the source part.
>>>
>>> Please, let me know what should I do to correct it and make real
>>> isotropic emission.
>>>
>>> Thanks,
>>> Joon Young Suk
>>>
>>> # S O U R C E S
>>> /gate/source/addSource rodsource0
>>> ###################################################################
>>> /gate/source/rodsource0/setActivity {activity} becquerel
>>> /gate/source/rodsource0/setType backtoback
>>> /gate/source/rodsource0/gps/particle gamma
>>> /gate/source/rodsource0/gps/energytype Mono
>>> /gate/source/rodsource0/gps/monoenergy 0.511 MeV
>>> /gate/source/rodsource0/gps/type Volume
>>> /gate/source/rodsource0/gps/shape Cylinder
>>> /gate/source/rodsource0/gps/radius 0.5 mm
>>> /gate/source/rodsource0/gps/halfz 25.0 mm
>>> /gate/source/rodsource0/gps/centre {rod0Xposition} 0. 0. mm
>>> /gate/source/rodsource1/gps/angtype iso
>>> /gate/source/rodsource0/gps/confine rod0_P
>>>
>>> /gate/source/addSource rodsource1
>>> ###################################################################
>>> /gate/source/rodsource1/setActivity {activity} becquerel
>>> /gate/source/rodsource1/setType backtoback
>>> /gate/source/rodsource1/gps/particle gamma
>>> /gate/source/rodsource1/gps/energytype Mono
>>> /gate/source/rodsource1/gps/monoenergy 0.511 MeV
>>> /gate/source/rodsource1/gps/type Volume
>>> /gate/source/rodsource1/gps/shape Cylinder
>>> /gate/source/rodsource1/gps/radius 0.5 mm
>>> /gate/source/rodsource1/gps/halfz 25.0 mm
>>> /gate/source/rodsource1/gps/centre {rod1Xposition} 0. 0. mm
>>> /gate/source/rodsource1/gps/angtype iso
>>> /gate/source/rodsource1/gps/confine rod1_P
>>>
>>>
>>
>> Joon Young Suk
>> Brain Research Centre
>> Dept. of Physics,
>> University of British Columbia
>> 2211 Wesbrook Mall
>> Vancouver, British Columbia
>> Canada, V6T 2B5
>>
>> joon at physics.ubc.ca
>> joonyoung.suk at gmail.com
>>
>> http://www.joonyoung.net
>>
>>
>>
>>
>
>
> _______________________________________________
> Gate-users mailing list
> Gate-users at lists.healthgrid.org
> http://lists.healthgrid.org/mailman/listinfo/gate-users
>
>
>
> From: Joon Young Suk <joonyoung.suk at gmail.com>
> Date: December 7, 2007 5:56:17 PM PST (CA)
> To: "Simon Stute" <gate.stute at gmail.com>
> Cc: gate-users at lists.healthgrid.org
> Subject: Re: [Gate-users] source angle type
>
>
> Thanks Simon,
>
> The two rod sources are confined in cylindrical shaped rods in a
> phantom, which is also cylindrical shaped. It doesn't show up
> clearly just because I set it as wire frame instead of solid volume
> for some reason. I used this confinement for the sources since the
> source will be moved during my simulation later.
>
> Anyway, I think I found the problem. As shown in the part of macro,
> I set the geometry of sources, which is not necessary for this case
> because the sources have been confined with other geometrical
> volume. So, I got rid of the geometrical setting part for two
> sources and now the display also look much better than before. I'll
> post the result from this simulation later if the result doesn't
> look beautiful.
>
> Best regards,
> Joon Young
>
> On 7-Dec-07, at 5:20 PM, Simon Stute wrote:
>
>> Hi Joon,
>>
>> Display is just display, not very faithful ... Have you got the
>> same results in your root results (or other kind of output
>> results) ??
>> I don't see any attenuation volume in your display, did you build
>> some ?? Because the 'confine' macro command is usually used to fix
>> an 'activity volume' to a geometrical volume (assigned with a
>> material) that is moving during the simulation. You have defined
>> some cylindrical shape activity volume but in your display, its
>> look like that it is a point source 'volume'. What is your
>> complete macro file ?
>>
>> Cheers,
>> Simon
>>
>> 2007/12/7, Joon Young Suk <joonyoung.suk at gmail.com>:
>>>
>>>>
>>>> Hi all,
>>>> I am trying to simulate the scan with a cylindrical phantom
>>>> which as two rod source inside.
>>>> I built two rod sources with cylindrical geometry and set the
>>>> angle type as "iso".
>>>> I think the LORs should be randomly distributed through all 4pi
>>>> angle, but the simulation doesn't look like that.
>>>>
>>>> From the display during the simulation, I can see most LORs are
>>>> lying horizontally on the centre plane.
>>>>
>>>> Please check the image from the followed link :
>>>>
>>>> http://www.joonyoung.net/iso.jpg
>>>>
>>>> Also, here is my code for the source part.
>>>>
>>>> Please, let me know what should I do to correct it and make real
>>>> isotropic emission.
>>>>
>>>> Thanks,
>>>> Joon Young Suk
>>>>
>>>> # S O U R C E S
>>>> /gate/source/addSource rodsource0
>>>> ###################################################################
>>>> /gate/source/rodsource0/setActivity {activity} becquerel
>>>> /gate/source/rodsource0/setType backtoback
>>>> /gate/source/rodsource0/gps/particle gamma
>>>> /gate/source/rodsource0/gps/energytype Mono
>>>> /gate/source/rodsource0/gps/monoenergy 0.511 MeV
>>>> /gate/source/rodsource0/gps/type Volume
>>>> /gate/source/rodsource0/gps/shape Cylinder
>>>> /gate/source/rodsource0/gps/radius 0.5 mm
>>>> /gate/source/rodsource0/gps/halfz 25.0 mm
>>>> /gate/source/rodsource0/gps/centre {rod0Xposition} 0. 0. mm
>>>> /gate/source/rodsource1/gps/angtype iso
>>>> /gate/source/rodsource0/gps/confine rod0_P
>>>>
>>>> /gate/source/addSource rodsource1
>>>> ###################################################################
>>>> /gate/source/rodsource1/setActivity {activity} becquerel
>>>> /gate/source/rodsource1/setType backtoback
>>>> /gate/source/rodsource1/gps/particle gamma
>>>> /gate/source/rodsource1/gps/energytype Mono
>>>> /gate/source/rodsource1/gps/monoenergy 0.511 MeV
>>>> /gate/source/rodsource1/gps/type Volume
>>>> /gate/source/rodsource1/gps/shape Cylinder
>>>> /gate/source/rodsource1/gps/radius 0.5 mm
>>>> /gate/source/rodsource1/gps/halfz 25.0 mm
>>>> /gate/source/rodsource1/gps/centre {rod1Xposition} 0. 0. mm
>>>> /gate/source/rodsource1/gps/angtype iso
>>>> /gate/source/rodsource1/gps/confine rod1_P
>>>>
>>>>
>>>
>>> Joon Young Suk
>>> Brain Research Centre
>>> Dept. of Physics,
>>> University of British Columbia
>>> 2211 Wesbrook Mall
>>> Vancouver, British Columbia
>>> Canada, V6T 2B5
>>>
>>> joon at physics.ubc.ca
>>> joonyoung.suk at gmail.com
>>>
>>> http://www.joonyoung.net
>>>
>>>
>>>
>>>
>>
>>
>> _______________________________________________
>> Gate-users mailing list
>> Gate-users at lists.healthgrid.org
>> http://lists.healthgrid.org/mailman/listinfo/gate-users
>>
>>
>
>
> From: Joon Young Suk <joonyoung.suk at gmail.com>
> Date: December 8, 2007 2:54:57 AM PST (CA)
> To: gate-users at lists.healthgrid.org
> Subject: [Gate-users] error on installation of lmf_v3.0
>
>
> Hi all,
>
> I'm trying to update gate from 3.0.0 to 3.1.2 with geant4.9.0.p01
> (from 4.8.1.p01). I've done this upgrade and now I'm trying to
> install LMF library.
>
> I got errors during compiling.
>
> Could you let me know what is my problem ?
>
> Macbook pro (2.16GHz, core duo, intel cpu)
>
> geant4.9.0.p01
> gate3.1.2
> i686-apple-darwin8-gcc-4.0.1
>
>
> Here is the log message :
>
> .
> .
> .
> gcc -I./includes/ -D_FILE_OFFSET_BITS=64 -fPIC -c -o obj/
> followCountRates.o src/followCountRates.cc
> gcc -I./includes/ -D_FILE_OFFSET_BITS=64 -fPIC -c -o obj/
> multipleCoincidencesSorter.o src/multipleCoincidencesSorter.cc
> gcc -I./includes/ -D_FILE_OFFSET_BITS=64 -fPIC -c -o obj/
> outputRootMgr.o src/outputRootMgr.cc
> src/outputRootMgr.cc:30:19: error: TFile.h: No such file or directory
> src/outputRootMgr.cc:31:19: error: TTree.h: No such file or directory
> src/outputRootMgr.cc:36: error: expected initializer before '*' token
> src/outputRootMgr.cc:37: error: expected initializer before '*' token
> src/outputRootMgr.cc: In function 'void outputRoot(const
> ENCODING_HEADER*, const EVENT_HEADER*, const GATE_DIGI_HEADER*,
> const EVENT_RECORD*)':
> src/outputRootMgr.cc:45: error: 'Double_t' was not declared in this
> scope
> src/outputRootMgr.cc:45: error: expected `;' before 'ownTime'
> src/outputRootMgr.cc:46: error: 'Int_t' does not name a type
> src/outputRootMgr.cc:47: error: expected `;' before 'timeMillis'
> src/outputRootMgr.cc:48: error: 'Float_t' was not declared in this
> scope
> src/outputRootMgr.cc:48: error: expected `;' before 'timeOfFlight'
> src/outputRootMgr.cc:51: error: 'Int_t' was not declared in this scope
> src/outputRootMgr.cc:51: error: expected `;' before 'gantryAngularPos'
> src/outputRootMgr.cc:52: error: expected `;' before 'sector'
> src/outputRootMgr.cc:53: error: expected `;' before 'sector1'
> src/outputRootMgr.cc:56: error: expected `;' before 'radial'
> src/outputRootMgr.cc:58: error: expected `;' before 'energy'
> src/outputRootMgr.cc:59: error: expected `;' before 'neighb'
> src/outputRootMgr.cc:66: error: 'pRootFile' was not declared in
> this scope
> src/outputRootMgr.cc:66: error: expected type-specifier before 'TFile'
> src/outputRootMgr.cc:66: error: expected `;' before 'TFile'
> src/outputRootMgr.cc:68: error: 'lmfTree' was not declared in this
> scope
> src/outputRootMgr.cc:68: error: expected type-specifier before 'TTree'
> src/outputRootMgr.cc:68: error: expected `;' before 'TTree'
> src/outputRootMgr.cc:69: error: 'nevt' was not declared in this scope
> src/outputRootMgr.cc:70: error: 'timeMillis' was not declared in
> this scope
> src/outputRootMgr.cc:71: error: 'timeOfFlight' was not declared in
> this scope
> src/outputRootMgr.cc:72: error: 'sector' was not declared in this
> scope
> src/outputRootMgr.cc:73: error: 'module' was not declared in this
> scope
> src/outputRootMgr.cc:74: error: 'submodule' was not declared in
> this scope
> src/outputRootMgr.cc:75: error: 'crystal' was not declared in this
> scope
> src/outputRootMgr.cc:76: error: 'layer' was not declared in this scope
> src/outputRootMgr.cc:77: error: 'sector1' was not declared in this
> scope
> src/outputRootMgr.cc:78: error: 'module1' was not declared in this
> scope
> src/outputRootMgr.cc:79: error: 'submodule1' was not declared in
> this scope
> src/outputRootMgr.cc:80: error: 'crystal1' was not declared in this
> scope
> src/outputRootMgr.cc:81: error: 'layer1' was not declared in this
> scope
> src/outputRootMgr.cc:83: error: 'energy' was not declared in this
> scope
> src/outputRootMgr.cc:84: error: 'energy1' was not declared in this
> scope
> src/outputRootMgr.cc:87: error: 'gantryAngularPos' was not declared
> in this scope
> src/outputRootMgr.cc:90: error: 'gantryAxialPos' was not declared
> in this scope
> src/outputRootMgr.cc:93: error: 'lmfTree' was not declared in this
> scope
> src/outputRootMgr.cc:93: error: expected type-specifier before 'TTree'
> src/outputRootMgr.cc:93: error: expected `;' before 'TTree'
> src/outputRootMgr.cc:94: error: 'nevt' was not declared in this scope
> src/outputRootMgr.cc:95: error: 'ownTime' was not declared in this
> scope
> src/outputRootMgr.cc:96: error: 'sector' was not declared in this
> scope
> src/outputRootMgr.cc:97: error: 'module' was not declared in this
> scope
> src/outputRootMgr.cc:98: error: 'submodule' was not declared in
> this scope
> src/outputRootMgr.cc:99: error: 'crystal' was not declared in this
> scope
> src/outputRootMgr.cc:100: error: 'layer' was not declared in this
> scope
> src/outputRootMgr.cc:101: error: 'radial' was not declared in this
> scope
> src/outputRootMgr.cc:102: error: 'tangential' was not declared in
> this scope
> src/outputRootMgr.cc:103: error: 'axial' was not declared in this
> scope
> src/outputRootMgr.cc:105: error: 'energy' was not declared in this
> scope
> src/outputRootMgr.cc:106: error: 'neighb' was not declared in this
> scope
> src/outputRootMgr.cc:108: error: 'gantryAngularPos' was not
> declared in this scope
> src/outputRootMgr.cc:111: error: 'gantryAxialPos' was not declared
> in this scope
> src/outputRootMgr.cc:146: error: 'nevt' was not declared in this scope
> src/outputRootMgr.cc:147: error: 'timeMillis' was not declared in
> this scope
> src/outputRootMgr.cc:147: error: expected `;' before
> 'getTimeOfThisCOINCI'
> src/outputRootMgr.cc:148: error: 'timeOfFlight' was not declared in
> this scope
> src/outputRootMgr.cc:152: error: 'sector' was not declared in this
> scope
> src/outputRootMgr.cc:152: error: expected `;' before 'pcrist'
> src/outputRootMgr.cc:153: error: 'module' was not declared in this
> scope
> src/outputRootMgr.cc:153: error: expected `;' before 'pcrist'
> src/outputRootMgr.cc:154: error: 'submodule' was not declared in
> this scope
> src/outputRootMgr.cc:154: error: expected `;' before 'pcrist'
> src/outputRootMgr.cc:155: error: 'crystal' was not declared in this
> scope
> src/outputRootMgr.cc:155: error: expected `;' before 'pcrist'
> src/outputRootMgr.cc:156: error: 'layer' was not declared in this
> scope
> src/outputRootMgr.cc:156: error: expected `;' before 'pcrist'
> src/outputRootMgr.cc:160: error: 'sector1' was not declared in this
> scope
> src/outputRootMgr.cc:160: error: expected `;' before 'pcrist'
> src/outputRootMgr.cc:161: error: 'module1' was not declared in this
> scope
> src/outputRootMgr.cc:161: error: expected `;' before 'pcrist'
> src/outputRootMgr.cc:162: error: 'submodule1' was not declared in
> this scope
> src/outputRootMgr.cc:162: error: expected `;' before 'pcrist'
> src/outputRootMgr.cc:163: error: 'crystal1' was not declared in
> this scope
> src/outputRootMgr.cc:163: error: expected `;' before 'pcrist'
> src/outputRootMgr.cc:164: error: 'layer1' was not declared in this
> scope
> src/outputRootMgr.cc:164: error: expected `;' before 'pcrist'
> src/outputRootMgr.cc:167: error: 'energy' was not declared in this
> scope
> src/outputRootMgr.cc:168: error: 'energy1' was not declared in this
> scope
> src/outputRootMgr.cc:172: error: 'gantryAngularPos' was not
> declared in this scope
> src/outputRootMgr.cc:175: error: 'gantryAxialPos' was not declared
> in this scope
> src/outputRootMgr.cc:177: error: 'lmfTree' was not declared in this
> scope
> src/outputRootMgr.cc:181: error: 'nevt' was not declared in this scope
> src/outputRootMgr.cc:182: error: 'ownTime' was not declared in this
> scope
> src/outputRootMgr.cc:188: error: 'timeMillis' was not declared in
> this scope
> src/outputRootMgr.cc:196: error: 'sector' was not declared in this
> scope
> src/outputRootMgr.cc:196: error: expected `;' before 'pcrist'
> src/outputRootMgr.cc:197: error: 'module' was not declared in this
> scope
> src/outputRootMgr.cc:197: error: expected `;' before 'pcrist'
> src/outputRootMgr.cc:198: error: 'submodule' was not declared in
> this scope
> src/outputRootMgr.cc:198: error: expected `;' before 'pcrist'
> src/outputRootMgr.cc:199: error: 'crystal' was not declared in this
> scope
> src/outputRootMgr.cc:199: error: expected `;' before 'pcrist'
> src/outputRootMgr.cc:200: error: 'layer' was not declared in this
> scope
> src/outputRootMgr.cc:200: error: expected `;' before 'pcrist'
> src/outputRootMgr.cc:205: error: 'radial' was not declared in this
> scope
> src/outputRootMgr.cc:207: error: 'tangential' was not declared in
> this scope
> src/outputRootMgr.cc:210: error: 'axial' was not declared in this
> scope
> src/outputRootMgr.cc:214: error: 'energy' was not declared in this
> scope
> src/outputRootMgr.cc:216: error: 'neighb' was not declared in this
> scope
> src/outputRootMgr.cc:218: error: 'lmfTree' was not declared in this
> scope
> src/outputRootMgr.cc: In function 'void destroyOutputRootMgr()':
> src/outputRootMgr.cc:226: error: 'lmfTree' was not declared in this
> scope
> src/outputRootMgr.cc:228: error: 'pRootFile' was not declared in
> this scope
> make: *** [obj/outputRootMgr.o] Error 1
>
>
>
>
> _______________________________________________
> Gate-users mailing list
> Gate-users at lists.healthgrid.org
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